rs10024717

Variant names:

• chr4-88298493-G-A
• rs10024717
• ENST00000500009.3:n.127-13303G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500009.3(PPM1K-DT):​n.127-13303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,066 control chromosomes in the GnomAD database, including 6,809 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6809 hom., cov: 33)
• Consequence: PPM1K-DT ENST00000500009.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

Genes affected

PPM1K-DT (HGNC:54093): (PPM1K divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPM1K-DT	NR_134236.1	n.133-13303G>A		intron_variant	Intron 1 of 4
PPM1K-DT	NR_134237.1	n.132+13432G>A		intron_variant	Intron 1 of 3
PPM1K-DT	NR_134238.1	n.133-13303G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPM1K-DT	ENST00000500009.3	n.127-13303G>A		intron_variant	Intron 1 of 4	1
PPM1K-DT	ENST00000652965.1	n.311-13303G>A		intron_variant	Intron 1 of 4
PPM1K-DT	ENST00000661337.1	n.81-13303G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43112 AN: 151948 Hom.: 6808 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0159

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.295

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.284 AC: 43123 AN: 152066 Hom.: 6809 Cov.: 33 AF XY: 0.277 AC XY: 20576 AN XY: 74328

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.294

Alfa AF: 0.336 Hom.: 5302

Bravo AF: 0.273

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10024717; hg19: chr4-89219645;